The second half of a two-part episode, it is most notable for featuring the beginning of the Dominion invasion of the Alpha Quadrant. It features the return of several familiar faces, drawing on plot lines from the third-season's "Improbable Cause" and "The Die is Cast", the body of the fourth season, and fifth-season opener "Apocalypse Rising".

Having just come through the wormhole in the closing moments of the previous episode, the Dominion fleet momentarily pauses and faces off with DS9, USS Defiant, several runabouts, and Gul Dukat aboard a Bird of Prey. The fleet then heads to Cardassian space, with Dukat's Bird of Prey following them. Thinking that he is trying to make a heroic stand against the entire fleet, Kira tells him to stand down, but Dukat informs her that he has been secretly negotiating with the Dominion for several months now, and that the Dominion has accepted Cardassia as a member, with Dukat as the leader of the new government.

At the internment camp, the prisoners are told of Cardassia's new allegiance, and all Cardassian prisoners at the camp are set free. As Garak walks off with the other Cardassians, he is told that he is to remain in prison, at the personal request of Dukat. Dukat himself appears in a video transmission to all of Cardassia, and pledges to expel Klingons and Maquis from Cardassian space and reclaim "all that was lost".

Elim Garak begins work on modifying the transmitter to contact the runabout in orbit over the internment camp, and Worf is selected as an opponent for Jem'Hadar to practice hand-to-hand combat. He is matched first against the youngest and least experienced of them, who scores an initial knockdown, but is eventually defeated. Meanwhile, Dukat has kept his promise to expel the Klingons, and they end up at DS9, where Gowron comes aboard to meet with Benjamin Sisko. Sisko suggests that they join to fight the real enemy - the Dominion - and Gowron agrees to reinstate the Khitomer Accords.

At the camp, Worf's subsequent Jem'Hadar opponents become successively older and more experienced, yet he continues to be victorious. Garak begins to suffer from claustrophobia, and Bashir suspects that he will be unable to complete the transmitter modifications. Worf returns to the cell from a day of fighting, and Bashir tells him he has several broken ribs and, along with Martok, encourages him to stop fighting. Worf's refusal to give up inspires Garak to overcome his fears and return to work.

Meanwhile, the station crew are awaiting reinforcements and trying to locate the Changeling in their midst. Dukat contacts Sisko and encourages him to persuade the Federation to join the Dominion. Sisko refuses, and Dukat reminds him that when he said he wanted to reclaim all lost Cardassian territory, which includes Deep Space 9, as it was built by Cardassians (although Sisko points out that it was built by Bajoran slave labour). Ignoring Dukat, Sisko deploys the Defiant and the runabouts to fight the incoming joint Cardassian/Dominion fleet. The Changeling Bashir is on one of the runabouts, having incapacitated the crew. O'Brien detects a fleet of ships decloaking, and the crew is shocked to discover Romulan warbirds instead of the expected Dominion fleet. The Romulans ask for permission to join the Federation/Klingon fleet, and Sisko grants it.

Back at the internment camp, as Worf is fighting the Jem'Hadar commander, three Jem'Hadar enter the cell and question the prisoners about the whereabouts of Garak, who has not been seen in some time. They discover the loose wall panels, and come close to discovering Garak when the prisoners successfully overpower their guards. In the combat ring, Worf is clearly defeated, but refuses to yield. Ikat'ika, the Jem'Hadar commander, is impressed by Worf's determination to fight to what ultimately would be his death; Ikat'ika himself yields the fight, saying that he can't defeat Worf - only kill him - and Ikat'ika is uninterested in that. This enrages the Vorta, who orders Ikat'ika's immediate execution. As the troops turn their guns to Worf, Garak manages to engage the transmitter, and they are beamed away to the orbiting runabout at the last second along with a Romulan captive.

Once on the runabout, the real Bashir sends an urgent message to DS9. The crew realizes that the Changeling Bashir is on a runabout and is carrying a bomb that he intends to detonate inside the sun, which will cause a supernova and incinerate DS9, Bajor, and the combined Starfleet, Klingon, and Romulan forces. The Defiant takes the risky maneuver of engaging warp drive within a solar system, and pulls up alongside the runabout and engages the tractor beam, pulling the runabout away from the sun at the last minute. The bomb explodes, destroying the runabout and the Changeling Bashir. Suddenly, the approaching Dominion fleet disappears from the sensors, and the crew realizes the fleet never left Cardassia - the Changeling had been broadcasting fake warp signatures.

Garak, Worf, Bashir, and Martok are reunited with their friends and loved ones on the station, and Sisko finalizes the new peace treaty with the Klingons. The revised version calls for a permanent Klingon presence on DS9, and Sisko selects Martok to command those troops.